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223 Cards in this Set

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# of gametes from a triploid producing that will be haploid?
(1/2)^n, n= # chromosomes
Monosomy
2N-1
Nullisomy
2N-2
Trisomy
2N+1
Tetrasomy
2N+2
euploid
an organism or cell has one complete set of chromosomes or an exact multiple of complete sets
aneuploid
an organism or cell has a chromosome number that is not an exact multiple of the haploid set of chromosomes.
autopolyploidy
all the sets of chromosomes originate in the same species
Example of autopolyploidy (think of a fruit we talked about in class)
3n banana- diploid fused with haploid.
allopolyploidy
the sets of chromosomes involved come from different, though usually related, species
Example of allopolyploidy animal (think horses and donkeys)
Mule- sterile
How can allopolyploid hybrids be fertile?
Rarely, through a division error, the two sets of chromosomes double, producing 2N1 + 2N2. Each diploid set can function normally in meiosis, so such fusion of two gametes can produce fully fertile, allotetraploid, 2N1 + 2N2 hybrids.
epigenetics
a heritable change in gene expression that occurs without a change in DNA sequence
Barr body
a highly condensed mass of chromatin
genetic mosaic
Some cells show the phenotypes of one X chromosome, and the other cells show the phenotypes of the other X chromosome. (Mammalian females that are heterozygous for X-linked traits are genetic mosaics due to X inactivation.)
Example of genetic mosaic
calico cats- orange parent and black parent
# Barr bodies = ?
# X chromosomes - 1
dosage compensation
in female mammals, inactivating one of the two X chr0s in somatic cells at an early state in development, leaving only 1 X chr0 transcriptionally active.
convergent evolution
similar phenotypes can evolve in organisms that are distantly related
rooted tree
where it is possible to distinguish one internal node as representing a common ancestor to all the other nodes on a tree
Gene conversion
the DNA sequence of an allele on one homolog is copied and replaces the DNA sequence of the allele on the other homolog (a process of genetic recombination in meiosis) (non-reciprocal)

Eg. A allele on one homology replicates and replaces the a alele on the other homolog, resulting in both homologs now having A alleles.
Parsimony-Based Approach
assume that the simplest tree (one with the fewest # of mutations) is considered to be the best and is deemed a tree of maximum parsimony.
Anaphase I
homolog separation is initiated by loss of sister chromatid adhesion
Coefficient of Coincidence
(#Obs d-COs)/(# Exp d-COs)
Interference Complete
Interference = 1, within 10 mu. No COs within 10 mu
Anaphase I
homolog separation is initiated by loss of sister chromatid adhesion
Coefficient of Coincidence
(#Obs d-COs)/(# Exp d-COs)
Interference Complete
Interference = 1, within 10 mu. No DOUBLE COs within 10 mu
Accurate genetic map
No 2 adjacent markers should be greater than 10 mu apart
NPD << PD
Genes are cis-linked
NPD = PD
Genes are on different chr0s (trans/repulsion)
# COs to get PD?
0
# COs to get NPD?
a double crossover results in a fraction of NPD (unless it only involves two of the chromatids)
Recombination Frequency
(NPD/Total) x 100%
Gene conversion & crossing over
About 50% of the time conversion is associated with a CO
1st gene mapped using modern DNA technology
Huntington's Disease gene
Human genome
3,000 x 10^6 base pairs
Polymorphism
presence of more than 1 common form in a population (eg. height)
Restriction enzymes
recognize specific DNA sequences (usually palindromic)
Southern Blotting
1. Digest DNA w/ restriction enzyme
2. Sep fragments with Gel Electrophoresis
3. Denature DNA by soaking gel in base sol'n
4. Blot DNA onto nitrocellulose (binds ss-DNA but not ds-DNA). Single-strand DNA migrates up nitrocellulose.
5. Block filter by incubating nitrocellulose with a vast excess of ss-DNA
6. Hybridize filter to a ss-radioactive "probe" DNA derived from a human DNA clone. Probe will stick to complementary ss-DNA.
7. Wash blot, expose it to film & develop film
autoradiogram
film after being exposed to Southern blot with radioactive probe on it
Founder effect
alteration in allele frequency due to the founding of a population by a small # of individuals.
Huntingtin Protein
run of glutamines encoded by CAG.
Normal run: 10-35
HD protein: 42-121
Polyglutamine
run of glutamines
Drosophila's salivary gland chromosomes?
# chromosomes in each cell?
Permanently in Interphase. Undergo 10 rounds of replication with no cell division.
2^10 = 1024 chromatids/chr0s in each cell
del(5)p15/+ (heterozygote)
show cri du chat
Heterozygotes for deficiencies are typically Normal/Abnormal?
Abnormal
Complementation
production of normal phenotype when 2 mutations are combined in trans in diploid
Crossing-over at telomeres and centromeres increase/decrease
Decrease. Suppressed.
multigene families
sets of related genes that have evolved from some ancestral gene through gene duplication
unequal C-O
misalignment of sequences during CO between homologs, causes gene duplications and deletions
Colorblindness caused by?
unequal CO
Paracentric Inversion
both breakpoints lie on same side of centromere
Pericentric Inversion
the breakpoints lie on opposite sides of centromere
Drosophila males CO or no?
No COs
Paracentric inversions appear to express/suppress CO?
Suppress. Non-CO chromatids are directed to the functional egg nucleus
Pericentric inversions appear to express/suppress CO?
Suppress because inviable progeny die and aren't seen
Heterozygosity for Pericentric Inversions reduce fertility or no?
Reduce fertility
CO occurs in which phase?
Pachytene
Adjacent I segregation
TI + N2 <--> T2 + N1
Adjacent II segregation
TI + NI <--> T2 + N2
Adj I + Adj II = ?
1/2 of segregation
Alternate Segregation
TI + T2 <--> N1 + N2
Adjacent Segregation chiasma shape
planar ring
Alternate Segregation chiasma shape
figure-8
Adj & Alt Segregation Progeny Results? (Viable and inviable ratio)
account for 50% but all progeny die (they did Adj Segregation)
50% but all progeny live (they did Alt Segregation)
Translocation hetero x Normal --> Progeny appearance/ratio?
50% zygote death, see semi-sterility
pseudolinkage
Apparent linkage of genes that are on different chr0s. Occurs because the zygotes that didn't inherit the genes together died and aren't seen.
2n + large duplication = dead/alive?
Dead. Lethal.
2n + whole haploid set = Dead/alive?
Often viable
colchicine
binds to tubulin (monomer of microtubles). Prevents the polymerization of tubulin. No spindle = No mitotic division
How to control euploids?
Treat euploid with colchicine so that cell goes through replication without division. When ready to see new euploid, wash out colchicine.
Eg 1. 2n cell + colchicine ---> 4n (wash out colchicine) ---> see 4n (2 4N daughters)

Eg 2: 2n cell + colchicine ---> 4n...+ colchicine ---> 8n...+ colchicine ---> 16N...wash out colchicine ---> See 16N.
Univalents
unpaired chr0s in Prophase I
Robertsonian
Long arm of chr0-14 (or 15) translocated and fused to chr0-21
Amniocentesis
stick a needle in uterus to get amniotic fluid of baby (at 16-18 wks)
Women- oocytes stop at which step? What is happening?
Oocytes get to diplotene and arrest. At diplotene, chr0s repel from each other but centromeres are holding chr0s together
What happens to woman's oocytes after age 40?
Homologs in Diplotene stage fall apart and meiosis is not correct (lose bivalents)
Heterochromatin
chromosomes that remain condensed throughout cell cycle
Facultative heterochromatin
Heterochromatin condensed in some cells but not others. Represents inactivated segments of euchromatin.
Eg. Barr body (inactivated X chr0 in somatic cells of XX mammalian females)
Constitutive heterochromatin
always condensed in Interphase. Located near centromeres. Present in all cells at identical positions on both homologous chr0s of a pair. (Centromeres and telomeres)
Goal of Evolutionary Theory
A scientific explanation for natural history of life
2 "Threats" of Evolution as a Scientific Theory (Name the guy too)
(Lewentin 2005)
1. "Fit of hostility"- Creationist challenge
- Fundamental belief
2. "Fit of enthusiasm"- expands explanatory scheme to human culture and ideas
Darwin's birthday
2/12/1809
Darwin was rich/poor? How?
Rich- inherited his mother's and cousin (his wife)'s fortune
Name of his fortune?
Wedgewood Pottery fortune
Darwin's occupation
Independent Industrialist
What was the name of society/culture of Darwin?
Industrialist Revolution
What role did Darwin play on the Voyage of the Beagle? Purpose of trip?
a. "Naturalist"
b. To map out shipping routes back to England
2 books Darwin brought on the Beagle journey?
Principles of Geology by Lyell and Milton's Paradise Lost
Main idea associated with Lyell and Geology?
Uniformitarianism
Uniformity of Law
the assumption that laws of chemistry and physics are unchanged through earth's geological history
Uniformity of Process
familiar geological processes to explain past events
Gradualism
Idea that geological changes (mountains, sea, grand Canyon) occur in small increments, which accumulate through time to produce large changes.
Another definition: denotes testable hypotheses both in Lyellian geology and Darwinian evolutionary biology
Catastrophism (name of guy?) definition
big, abrupt changes in geology
(Cuvier)
Non-directionalism
dynamic steady state
What happened at the Cretaceous-Tertiary boundary?
a point in geological records of mass extinction- extinction of dinosaurs
How to determine how long ago clay was deposited at Cretaceous-Tertiary (K-T) boundary?
Measure the amount of iridium in clay. (Iridium comes every year from meteor rock)
Theory of Impact Crises
There was an asteroid bombardment onto the Earth that caused a ton of iridium to be on Earth all of a sudden (messed up geological dating by using iridium)
Domain of Darwinism
diversity of plant and animal life after it was formed
(NOT origin of life theory)
Neo-Darwinism
Darwinism and chromosomal theory of Inheritance
- rejects Lamarckism = ?
Larmarkism: that acquired characteristics are inheritable
Who was Thomas Huxley ?
Darwin's advocate/ Darwin's Bulldog
What did Thomas Huxley assert?
Supernatural is not a part of current science
developmental module
characteristic pattern of gene expression and cellular proliferation/differentiation subject to evolution by heterotopy
SNP
polymorphism for single base pair change
population
focal of Darwinian evolutionary processes
hybrid DNA
contains DNA strands from 2 different homologs
transposition
insertion of chromosomal segment into new location
synapomorphy
diagnostic criteria for a clade
polytene band
chromomere
CVS
Chorionic villus sampling) sampling of fetal tissue from placenta
uniformitarianism
denotes Lyell's principle of geology
5-methylcytosine
produced by DNA methyltransferase after DNA replication
chromatid interference
lack of responsibility for recombination frequency 50% at maximum. (States that recombination freq can equal 100%)
Does this exist?
No.
q
long arm
telomere
present at normal chromatid ends
constitutive heterochromatin
condensed in interphase of all cells
Active doubt
test Darwin's explanations, correct errors
Who came up with this?
Thomas Huxley
Hypothetico Deductivism (falsification)
1. Gather data (observations about something that is unknown, unexplained, or new)
2. Hypothesize an explanation for those observations.
3. Deduce a consequence of that explanation (a prediction). 4. Formulate an experiment to see if the predicted consequence is observed.

Falsification: Theory can be contradicted by an observation or the outcome of a physical experiment.

Means falsification can disprove a theory. Doesn't mean theory is wrong though
Construct theory
rational explanation based on measurable natural phenomena
Positive Proof: Yes/No
No positive proof.
Parsimony
simplest explanation is the best working hypothesis
Complementary Principle
there are both subjective and objective components to measurement
- Subjective Component (volition):
- Objective Component (Cognition):
Subjective: Questions asked, concepts chosen, measurements chosen
Eg. Electron as a particle and a wave (dual ideas of a single entity)
Objective: measurements taken represent the dynamics of the system being studied
5 Principles of Ernst Mayr
1. Evolution as such: The biological world is neither constant nor perpetually cycling, but is steadily and perhaps directionally changing.
2. Common Descent: "all plants and animals have descended from some one form into which life was first breathed"
3.
Populational belief
Population is the lowest level of biological complexity that evolves.

Population is the basic unit of evolutionary change.
Lineages
Ancestor-descendant populations of a series through time
4 Events:?
1. Persist without change
2. Persist with change
3. Branch
4. Go extinct
Divergence of character
separate lineages accumulate differences from their common ancestor and from each other
Phylogeny
the structure of evolutionary history is a branching tree of lineages
Biogenetic law
Who made this up?
"ontogeny recapitulates phylogeny"
Ernst Haeckel
Terminal addition
New features are added at the end of ontogeny
Ontogeny Condensation
Older features are displaced to earlier and shorter developmental occurrence
Ontogeny
development of an organism from zygote to adult
Which phylum are Humans in?
What trait is this phylum known for?
Chordata
Notachord trait.
What is this trait in humans today?
Remnants of notachord in humans are the disk bones in our vertebrate
Tunicates in which phylum?
Chordata
All animals share an early developmental stage. What is the order?
Zygote --> Blastula --> Gastrula
Heterochrony
evolutionary change in developmental rates and timing
Eg. Salamanders- aqua form in larvae stage, then terrestrial form in adult stage
Heterotropy
evolutionary change of physical location of a developmental process/module.
Eg. Geckos have toe pads on fingers and toes. (Modified scales) Toe pads initially evolved on toes and fingers but expressed in a different location (tails)
Modularity
characteristic, semi-autonomous patterns of gene expression and celluar proliferation and differentiation
Module
An evolving trait that eventually gives rise to other structures
Eg. Vertebrate tail
Who coined the word ecology?
Ernst Haeckel
Homology (who made this up?)
The same organ in different organisms under every variety of form and function

Richard Owens (1804-1892)
Evolutionary Homology
forms derived from an equivalent characteristic of a common evolutionary ancestor (molecular and cellular characteristics like homologous DNA)
ontogeny recapitulates phylogeny
Haeckel's principle for inferring phylogenies based on the conjectures that evolutionary change adds new features to the end of organismal ontogeny and condenses older features into earlier developmental stages
Caenogenesis
Haeckel's term for evolutionary aquisition of new characters at pre-adult stage directly rather than by condensation from an ancestral adult condition

Evolution of new characters that are added to pre-adult states (don't see some characters until adult stage)
Eg. Tadpoles --> Frogs, Caterpillar --> Butterfly
parsimony
Methodological principle that the simplest explanation of existing data is the favored working hypothesis; also specifically the phylogenetic principle that the tree structure requiring the smallest amount of character evolution is the best working hypothesis
Complementarity Principle
scientific principle derived from the quantum mechanics of Niels Bohr that a scientist must describe both the volitional (subjective) and cognitional ( objective) aspects of measurement
alignment
arrangement of homologous DNA sequences to identify specific site or positional homologies
evolution as such
Mayr's term for the most basic of Darwin's theories, that the biological world is neither constant nor perpetually cycling, but always changing
hypothetico-deductivism or falsification
Formal term for Huxley's prescription that Darwin's theories should be subject to "active doubt" by gathering data that could potentially reject Darwin's conjectures
common descent
Mayr's name for Darwin's theory that all our plants and animals have descended from one some form into which life was first breathed
convergent evolution
when phenotypes appear similar enough to have two species relation on a tree, but truly they are very genetically different (in older days only phenotypes were used to construct trees and this caused problems)
Excluding a three-way split, the number of alternative, phylogenetic hypothesis possible for any analysis of three ingroup species and 1 outgroup species is what?
three
Distance Methods
based on statistical principles that group things based on their overall similarity to each other.
Parsimony Approaches (to form trees)
group organisms in ways that minimize the number of substitutions that must have occurred since they last shared a common ancestor and are generally invoked only in molecular evolution studies
Maximum Likelihood(or Bayesian)
intrinsically probabilistic/statistical and have only become feasible for typical data sets as the raw power of computers increased
Molecular Homology
Homologous DNA (diagnosed by high sequence similarity and one copy per haploid genome)
Eg. Forelimb bone structure of chordates
Historical structure of sharing homologies
nested hierarchy of groups within groups
Eg. All those that share vertebrate and there are groups within these
sequence of homologous DNA
many comparisons between humans and chimps
15 million years ago
Before molecular homology- the # years ago that the most recent (believed) common ancestor for chimps and humans
5 million years ago
Now, thanks to molecular homology- the believed # years ago the most recent common ancestor for chimps & humans
Monophyletic group (clade)
a group of 2 or more species/lineages that includes the most recent common ancestor of all members of the group and ALL of its descendants
MRCA
most recent common ancestor
cladogram
branches denote nested hierarchy of clades as diagnosed by synapomorphies
phylogenetic tree
branches denote historical evolutionary lineages
Are apes a monophyletic group?
No, if we don't count humans
assume the simplest tree/ one with least mutations
parsimony method
Alignment
Hypotheses of site homology- usually easiest to align protein-coding DNA
ancestral state
present in ingroup and outgroup
derived state
present only in the ingroup
ambiguous
no sharing of character states between ingroup and outgroup
parsimony informative characters
shared derived characteristics
Parsimony criterion
Find the tree topology that requires the smallest # of evolutionary changes.
Genetic difference
% sequenced difference or % sequenced similarity
UPGM
averaging algorithm- quick way to get topology tree
transversion
pyrimidine for a purine and vice versa
transition
pyrimidine for a pyrimidine and purine for a purine
transition
A DNA substitution mutation, purine with purine (A<-->G) and pyrimidine with pyrimidine (C<-->T)
transversion
purine with pyrimidine and vise versa
Ratio of transversion to transition
Transition 10x more likely than transversion
Which position of codon is most likely to switch/
3rd position
Bayesian operation
calculate likelihood for contrasting trees
maximum likelihood method
evaluate the probability of observing the results in each of the columns considering all possible trees, and measure the likelihood of the entire data set for each contrasting tree.
2 parallel substitutions on a terminal branch vs. 1 substitution on an internal branch- Which is more likely? Exception?
2 parallel subs on a terminal branch is more likely (1 change) while 1 sub on internal branch resulted in 2 changes.
However, if the internal branch is shorter compared to the length of the terminal branches, then the 2 ways become equally likely
homoplasy
character similarity that does not represent common ancestry (homoplastic)
parallelism
lineages diverge from common ancestor but not from each other
reversal
evolutionary return to an ancestral character formerly changed or lost
convergence
origin of superficially similar features by dissimilar evolutionary processes- usually pertains to morphology
Wings are an example of ___ evolution?
Homoplastic evolution. Wings look similar among organisms but do not represent common ancestry
three major evolutionary domains
bacteria, eukarya, archaea
Transitions vs. Transversion- which is more homoplastic?
Transitions because character similarity (purine for a purine or pyrimidine for a pyrimidine) does not represent common ancestry
codon position
silent vs. replacement sites
genetic code is degenerate means?
20 AAs coded by 64 codons
Silent site
a codon letter may change but it doesn't change the AA it codes for
Replacement site
change in codon letter changes the AA it codes for
Which # codon does silent substitution?
Usually 3rd codon
Bayesian analysis
each internal branch gets posterior probability
Probability > or = to ? to get strong support?
p > or = 0.95
Bootstrapping
sample sites in an alignment with replacement to produce a new data set equal in size to the original one. For each clade/branch, what % of the trees contain the clade/branch?
If > or = 70%, reject original hypothesis that branch doesn't exist (?)
Allopatric speciation
geographic isolation precedes evolution of species differences
Outgroup
allows you to place the root somewhere among the ingroup
What's the outgroup in the Tree of Life?
Contains no outgroup because it contains all of life
endosymbiotic theory of eukaryote origins (who came up with this?)
mitochondria and chloroplasts are evolutionarily more similar to bacterial genomes than nuclear genomes (the genomes they are found in)
Lynn Margulis
Biological Species concept (who?)
(Mayr) a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature.

to determine whether two now distinctly different genetically and phenotypically populations should be considered separate species by testing for Reproductive Barriers
Niche
set of resources actually or potentially used by a population
Angelman syndrome
same genotype as Prader-Willi syndrome
variational theory
Darwinian evolution is a populational process operating on hereditary differences among organisms within a population
character polarity
ancestral-descendant relationships among alternative character states
5:3 segregation
postmeiotic segregation present
empirical verification
data support a hypothesis as the best working explanation
trivalent
usually present in the haploid number in autotriploid
algorithm
a process characterized by substrate neutrality, underlying mindlessness, and guaranteed results.
Eg. Natural selection
founder event
A SOURCE OF ALLOPATRY OF POPULATIONS CAUSED BY RARE DISPERSAL OF A FEW ORGANISMS ACROSS A PRE-EXISTING, STRONG GEOGRAPHIC BARRIER
parsimony informative/phylogenetically informative
the subset of variable characters in a phylogenetic analysis for which sharing of a derived state (synapmorphy) is observed.
phylogenetic species concept
a lineage of ancestral-descendant populations diagnosably distinct from other such lineages.
postzygotic barrier
a broad category of reproductive barriers in which hybrid offspring are inviable or sterile, or second-generation offspring suffer these problems
adaptation
a character that arose by national selection for a currently observed biological role
The kind of chromosomal evolutionary change needed to derive the human karyotype from one characteristic of other apes.
fusion or chromosomal fusion
A source of allopatry of populations in which formation of a geological barrier subdivides a formerly continuous population
vicariance
Exaptation
Shifts in the function of a trait during evolution
mathematical model
an equation that simplifies biological details to identify the critical parameters sufficient for predicting an outcome.
Blocking factor
binds to the X chromosome and prevents its inactivation
Gene-to-Centromere distance
(#2nd Div Segs)/(2 Total)